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相关概念视频

GTPases and their Regulation02:14

GTPases and their Regulation

Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell signaling, vesicular transport, and the regulation of cell shape and motility. Mutation or dysfunction of these proteins can lead to disease. There are around 40,000 known G-proteins that can broadly be classified into two groups ‒  small G-proteins consisting of a single domain and large multi-domain G-proteins.
Large G-proteins, also known...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Reporter Genes02:11

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
Commonly used reporter...
GTPases and their Regulation02:14

GTPases and their Regulation

Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell signaling, vesicular transport, and the regulation of cell shape and motility. Mutation or dysfunction of these proteins can lead to disease. There are around 40,000 known G-proteins that can broadly be classified into two groups ‒  small G-proteins consisting of a single domain and large multi-domain G-proteins.
Large G-proteins, also known...
Activation and Inactivation of G Proteins01:22

Activation and Inactivation of G Proteins

Heterotrimeric G proteins are guanine nucleotide-binding proteins. As the name suggests, heterotrimeric G proteins are composed of three subunits: alpha, beta, and gamma. They remain GDP-bound or GTP-bound inside the cells and switch between inactive/active states. The Gα subunit possesses the nucleotide-binding pocket that binds guanine nucleotides and switches between GDP or GTP-bound states. In contrast, the Gꞵ and Gγ subunits are always bound together with high affinity and are together...
Transducer Mechanism: G Protein–Coupled Receptors01:30

Transducer Mechanism: G Protein–Coupled Receptors

G Protein–Coupled Receptors (GPCRs) are membrane-bound receptors that transiently associate with heterotrimeric G proteins and induce an appropriate response to various stimuli. GPCRs regulate critical physiological pathways and are excellent drug targets for treating diseases such as diabetes, cancer, obesity, depression, or Alzheimer's. Nearly 35% of approved drugs implement their therapeutic effects by selectively interacting with specific GPCRs.
GPCRs are also called heptahelical, 7TM, or...

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相关实验视频

Updated: May 29, 2026

Visualizing Clathrin-mediated Endocytosis of G Protein-coupled Receptors at Single-event Resolution via TIRF Microscopy
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iGTP:学习可解释的细胞嵌入,以推断单细胞转录组的基础生物机制.

Kang-Lin Hsieh1, Kai Zhang2, Yan Chu3,4,5

  • 1Division of Cancer Medicine, Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, United States.

Briefings in bioinformatics
|June 24, 2025
PubMed
概括
此摘要是机器生成的。

一个新的可解释的生成转录程序 (iGTP) 框架模型转录程序和单细胞RNA测序数据的蛋白质-蛋白质相互作用. iGTP增强了生物洞察力,并预测了细胞对干扰的反应.

关键词:
图表神经网络的神经网络可以解释的深度学习.单细胞转录组学 单细胞转录组学转录程序是一个转录程序.变化的自动编码器.

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科学领域:

  • 计算生物学是一种计算生物学.
  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 像变异自编码器 (VAE) 这样的深度学习模型为单细胞转录组提供了低维的细胞嵌入.
  • 然而,在没有特定的结构设计的情况下,VAE往往缺乏具有生物意义的潜在空间.
  • 可解释模型对于理解复杂的生物系统至关重要.

研究的目的:

  • 开发一个新的可解释的生成转录程序 (iGTP) 框架.
  • 为了建模转录程序 (TP) 空间和蛋白质-蛋白质相互作用 (PPI) 在生物状态中的重要性.
  • 提高单细胞分析中潜伏表征的解释性和生物相关性.

主要方法:

  • 设计了iGTP框架,集成TP空间和PPI网络.
  • 使用基因本体学,正规途径和PPI数据库验证了iGTP.
  • 将潜层与图形神经网络 (GNN) 集成,用于扰乱响应推断.
  • 应用iGTP嵌入式与隐性扩散模型用于细胞类型特定的嵌入式生成.

主要成果:

  • iGTP阐明了基底真理细胞反应,并在功能丰富方面表现优于现有的方法.
  • 该框架成功地模拟了TP和PPI在各种生物环境中的重要性.
  • 当与GNN结合时,iGTP有效地推断出细胞对干扰的反应.
  • 潜在扩散模型使用IGTP生成了特定细胞类型和状态的精确细胞嵌入.

结论:

  • iGTP提供了一个强大的框架,用于单细胞转录组的可解释性分析.
  • 该模型在PPI和TP两级提供了洞察力,促进了生物学理解.
  • iGTP在预测应对新奇扰动的反应和产生细胞特异嵌入方面表现有前途.